Get organism from GenBank

Return the organism name for an accession ID.

Usage

gb_organism_get(id)

Arguments

id

character, sequence accession ID(s)

Value

named vector of definitions, if no results found NULL

See also

ncbi_acc_get()

Other get: gb_definition_get(), gb_fasta_get(), gb_record_get(), gb_sequence_get(), gb_version_get()

Examples

library(restez)
restez_path_set(filepath = tempdir())
#> ... Creating '/tmp/RtmpWQaZTT/restez'
#> ... Creating '/tmp/RtmpWQaZTT/restez/downloads'
demo_db_create(n = 5)
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpWQaZTT/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
(org <- gb_organism_get(id = 'demo_1'))
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpWQaZTT/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#>              demo_1 
#> "Unreal organism 1" 
(orgs <- gb_organism_get(id = c('demo_1', 'demo_2')))
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmpWQaZTT/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#>              demo_1              demo_2 
#> "Unreal organism 1" "Unreal organism 2" 


# delete demo after example
db_delete(everything = TRUE)